The neXtProt knowledgebase in 2020: data, tools and usability improvements

Monique Zahn‐Zabal(SIB Swiss Institute of Bioinformatics), Pierre-André Michel(SIB Swiss Institute of Bioinformatics), Alain Gateau(SIB Swiss Institute of Bioinformatics), Frédéric Nikitin(SIB Swiss Institute of Bioinformatics), Mathieu Schaeffer(University of Geneva), Estelle Audot(SIB Swiss Institute of Bioinformatics), Pascale Gaudet(SIB Swiss Institute of Bioinformatics), Paula Duek(SIB Swiss Institute of Bioinformatics), Daniel Teixeira(SIB Swiss Institute of Bioinformatics), Valentine Rech de Laval(University of Geneva), Kasun Samarasinghe(University of Geneva), Amos Bairoch(University of Geneva), Lydie Lane(University of Geneva)
Nucleic Acids Research
October 18, 2019
10.1093/nar/gkz995
Cited by 225Open Access
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Abstract

The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describe the incorporation of three new data sets that provide expression, function, protein-protein binary interaction, post-translational modifications (PTM) and variant information. New SPARQL query examples illustrating uses of the new data were added. neXtProt has continued to develop tools for proteomics. We have improved the peptide uniqueness checker and have implemented a new protein digestion tool. Together, these tools make it possible to determine which proteases can be used to identify trypsin-resistant proteins by mass spectrometry. In terms of usability, we have finished revamping our web interface and completely rewritten our API. Our SPARQL endpoint now supports federated queries. All the neXtProt data are available via our user interface, API, SPARQL endpoint and FTP site, including the new PEFF 1.0 format files. Finally, the data on our FTP site is now CC BY 4.0 to promote its reuse.

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